MIDI Parts in folders don’t inherit their colors from the Track colors properly.
A MIDI Track without any color assigned to it and outside a folder inherits properly the color of the MID Track family which you can set in preferences
A MIDI Track without any color assigned to it and inside a folder gets a generic color of some kind
When you move the Track outside the Folder the part changes color
[edit]
This works for Audio Parts too.
Not the end of the world as we know it, buuuut …